Ruby's Secret (Rewritten)
by Aubrie1234
Summary: When a new evil team comes to the surface from the ashes of teams Aqua and Magma, Team Steam, the PokeDex Holders are more than willing to take it down. However, Ruby has disappeared and Archie and Maxie want to help the kids destroy the new team. Where is Ruby, and do the men have another motive?
1. Chapter 1

Ruby's Secret (Rewritten)

By: Aubrie1234

* * *

"Well well well, look what we have here!" A black-haired and blue-eyed girl gazed down on a boy tied to a chair. The boy was beaten and bruised, blood trickling from his mouth; his crimson red eyes glared immensely at the girl. Behind the chair was the door to the dark room, open with the silhouette of another boy in the doorway. The boy was the brother of the girl, having red hair and eyes, and the girl was more tanned than her twin. They wore regular clothes, such as jeans and shirts, but the jackets had a strange logo on them: they were completely black, except for the logo on the front, which was of a brown volcano spewing out white steam, which shaped into crossbones. The girl was grinning greatly as her brother only watched, the boy in the chair silent and glaring. The boy once wore a hat, but it was no where in sight, showing his hair. It was white on both sides, with a black streak in the middle, and along the left of his hairline, there were two pale scars, side-by-side.

"Kid, it'd be best if you talk." the boy in the doorway said, "Or do you want to be beaten again?" The boy's hand trailed down to his side, where a whip hung in its holder on his belt, curled at rest. A strangled growl escaped the tied boy's mouth, and the girl clapped.

"Could I watch this time, brother?" she asked. The boy in the doorway sighed and removed the whip from the holder, holding the thong tightly in his hands.

"No." The girl made a frustrated sound, but left. The steel door slammed behind her and a light flickered on above the two boys.

"Why?" the boy in the chair finally said, his voice raw and quiet, "You're not on her side. You don't want this." There was a crack and a great stinging sensation on the tied boy's arms.

"You have no idea what I think." the other boy once again took the whip in both hands, "Now, how did you know?"

"How could I not? You guys aren't exactly subtle." Another crack and the tied boy now had a welt on his cheek.

"There's more to it, I know." the redhead said, "Just give me the answers and I'll let you go."

"Yeah right." the white- and black-haired boy gave a small, bitter laugh, "Now that you have me, there's no chance you're going to let me go. Not only am I a good hostage for what you're planning, but you need me to put your plan into action, don't you?" The redhead's eyes narrowed.

"Well then." he returned the whip to its holder on his belt, "Let's see if you talk after another day of no food." The echo of the door closing once again and the lamp flickering out reminded the tied boy of the circumstances that had gotten him here, as he had been there for two days already. He only hoped that his friends didn't come to rescue him, as they would only walk into the trap Team Steam had arranged, with his unwilling help.

* * *

"Anything, Magnus?" The girl asked as her brother closed the door.

"Not yet, Arianna. I'm sure he will, though, if not soon." Magnus walked on down the corridor, Arianna following closely. They passed by a large window of glass, which gazed down into a lab, where several scientists were working under the watchful eyes of some grunts, all of them older than the siblings and wearing similar jackets.

"Why doesn't he see it?" Arianna sighed, "With his help, we would make the world a better place."

"Give him time. He'll come around eventually." They then passed another large window, which showed a giant steel room, devoid of anything.

"Not soon enough."

"We still have time. Time that can be used to put our plan into action. However, he knows about our plan, I'm sure."

"It hasn't changed, so why wouldn't he?" Magnus hummed.

"Good point. But, as long as he's stuck in there, he won't be able to do anything about it."

"And we can't do anything, either." Arianna argued, "Until he comes to our side, we can't make a move."

"We'll keep trying. If we can't turn him over with intimidation," Magnus made a familiar grin, "Then we'll force him. Have the scientists start working on a collar that can control him and him alone, and be able to fit him in whatever form he becomes." Arianna smiled.

"Alright. And when do you think his friends will notice?"

"Soon, if they already haven't. Green is quite the social butterfly, you know. If she doesn't get into contact with our little _friend_ , then all of the PokeDex Holders will know in less than a day." Arianna then dropped her smile.

"What about Archie and Maxie?" Magnus lost his grin.

"Nothing right now. If they tip their hand, we'll take the opportunity to get rid of them before they derail the plan."

"What do you think they'll do once they learn of us?" Magnus shrugged.

"Who knows? They certainly won't like us, that's for sure. But," the grin returned, "We can outfox them, because we know _exactly_ what they'll do before they do it." Arianna giggled.

"You're certainly confident." she said, "You don't think anything will go wrong?"

"Of course _something_ will go wrong, but most of it is under control. Soon enough, we will have Hoenn under our thumbs, and then the rest of the world will follow, with or without the legendary pokemon. Everyone will fear us, and no one will be brave enough to take us down, once the PokeDex Holders are out of the way."

* * *

 _ **Well, what do you think of my rewritten version? In the original, I seriously had no idea where I was going. Now, I have a little bit of an idea of where it's going to go, with an ENTIRELY DIFFERENT storyline. I hope you like it, so read and review!**_


	2. Chapter 2

Ruby's Secret (Rewritten)

By: Aubrie1234

* * *

Upon not being able to contact Ruby for two days, Green grew worried. Usually, the boy was one of the few Dex Holders who kept in touch every single day; however, every time the girl called, it went straight to voicemail. She had dismissed it the first few times as Ruby being busy, going to call back later. But, when there was no call the next day, that was when Green began to worry. It only increased when she called his house.

"Green!" Ruby's mother sounded scared, almost, and out of breathe somewhat.

"Is something wrong, Mrs. Maple?" the PokeDex Holder asked.

"Yes," what she said next confirmed Green's fears, "Ruby's been missing for two days!"

"Did he leave a note?"

"No! He went out to the forest to train his pokemon, but never came back! Sapphire and Emerald are out looking for him, and I haven't been able to tell Norman, but-"

"I know." Green interrupted, "Would it make you feel better if the other Dex Holders and I came over to help?"

"Yes! As soon as possible!"

"We'll be right over. Bye." Green then hung up and began to call the other Dex Holders, from Kanto to Unova. Surely they weren't dealing with another evil team or problem, just some simple kidnapping.

But things sometimes don't turn out to what you them to be, do they?

* * *

"No..."

"Things are coming together, aren't they?"

"Don't hurt them, _please_."

"They are the main things standing in our way to ruling the world, besides you, Archie, and Maxie. So, I think you know the answer." The tied boy was silent, glaring at his captors with all he could muster. Arianna was holding a tape recorder, which had just played the phone conversation.

"Besides, in a few days, everything will change. The PokeDex Holders will be dead, and at _your_ hands. Or should that be paws?" Magnus grinned at the growl he got from the boy.

"You know I'll never do it." the boy defiantly proclaimed.

"Not of your own accord, no." Arianna said, "Unless you were brainwashed or lost your memory. But, instead, we have a _much better_ idea of how to get you to work for us." The boy glanced between them worriedly, wondering if he would get an explanation.

"Not yet, Frost." Magnus slid a hand through the tied boy's hair, just to watch him shiver, "But soon. Very, _very_ soon."

* * *

"Where can ya be, ya stupid Prissy Boy?" Sapphire muttered under her breath as he swung through the trees. Chic jumped through the trees with her, helping to look, as Emerald, riding on his Sceptile, looked and followed below. When Ruby had not been seen by her for two days, Sapphire had not thought much of it. She thought he had done it to avoid her after their last fight, but upon hearing how no one else had seen him, especially from his own mother, was when Sapphire worried. After their adventure with the 80-day challenge, Ruby had made it an objective to spend as much time with his family as possible, mostly to held amend the relationship with his father, despite Norman not being home most of the time. So, with him not going home for two days, it was a troubling matter.

Emerald, not knowing Ruby as well as Sapphire, had started to worry after the first day. When Sapphire asked why, he justified it with: "I can feel it. You're in tune with nature, and especially Ruby, so why can't you?" That had made her question whether or not she really had as good a relationship with her newly-returned best friend (and crush) as she had thought. If Ruby had been kidnapped or something happen to him, wouldn't she have gotten a feeling about it, as Emerald had? It confused her to no end, and she got increasingly agitated at being confused; like her father, she wanted to know things, and not knowing things... well, it was one way to set off her already hair-trigger temper. Everyone knew this, which is why Emerald and even the pokemon left her to her thoughts, so they wouldn't be the targets of her frustration, once she decided to unleash it. Only Chic was unaffected, and partially Ruby. The Blaziken could take her master's frustration unscathed, and Ruby... Let's just say his Running Shoes come in handy quite a lot when he tries to ease an angry Sapphire.

 _At least it helps vent my frustration._ the wild girl thought, _But just where is he?_ Emerald was having the same thoughts. The two pokemon, of course, were worried for Ruby, but mostly for their best friend, Mumu. With Chic's sometimes aggressive personality and Sceptile's sarcastic remarks, they would occasionally get into fights, at which Mumu had to separate and calm them. It was one of the things they loved about their friend, who never wanted to fight and broke them up, but would fight if he had to; of course, he was never happy about it, like his trainer. Mumu had also been a part of their trio, back when they were only a Mudkip, Torchic, and Treecko, before the region-changing 80-day challenge/journey started.

Chic had been about to start remembering the old days when a branch smacked her in the face, reminding her where she was and what she was doing. Below, Sceptile let out a loud snicker, but Chic ignored it. All four continued their search for their missing friends, hopeful that they would be found, safe. Sapphire was even having thoughts that Ruby had somehow gotten lost in the forest and even with his pokemon, had no way to get back. It was pretty impossible, though, as all of his pokemon knew the way back to Littleroot. The girl was still hopeful, though, and already had thoughts on how to tease the ruby-eyed boy, once he was found. Hey, a girl can dream, can't she?

Their hopes were dashed, however, when Sceptile picked up on the scent of a Stun Spore and went to investigate, dragging Emerald with him, as the boy was riding on his back. Sapphire and Chic, not wanting to separate, followed from the trees. They came upon a clearing and everyone stopped in shock at what they saw, petrified.

"Oh no..."

* * *

It was a day later when all the Dex Holder had gather before Ruby's house, in Hoenn. Gold, of course, didn't think it was as serious as Green though, where Crystal had to drag him along, and White could barely keep up with Black as he flew to Hoenn on his Braviary, Brav; she had finally managed to catch up to him before he left Unova completely, as she did not have her own pokemon to carry her such a distance.

"Okay, listen up!" Green said, getting everyone's attention, "We're here to help find Ruby, so no shopping," she winced at that part, "no gambling," Gold grumbled to himself angrily, "and no battling unless we have to, including training." She eyed Red, Blue, and Black especially.

"But don't you think everything seems suspicious?" Silver asked, "Who would want to kidnap only _one_ Dex Holder?"

"You're forgetting the rest of Ruby's titles." Pearl said, "Even if he hadn't been a PokeDex Holder, he's also a Contest Master _and_ the son of a Gym Leader. That's enough for kidnappers already."

"You're the son of the Tower Tycoon in the Sinnoh Battle Frontier and can recognize what move a pokemon will use next, just by their movements." Blue shot back, "Besides being Dex Holders, _all_ of us have titles that would make us perfect kidnapping material, if someone managed to kidnap us."

"But Ruby is really powerful; like, almost on the Kanto Dex Holders' levels, and that's saying something." White said, "So, who could have kidnapped _him_?"

"We're here to find out, aren't we?" Crystal said as Green knocked on the door. There was the shuffling of feet before the door opened, showing Ruby's mother. The woman had a crumpled tissue in one hand and her eyes were red. It was obvious she had been crying, so the PokeDex Holders tried to go easy with her in their questions, though some were denser than others...

"Oh, Green!" she seemed to brighten just at the sight of them, "All of you, thanks again so much for coming!"

"Did Sapphire and Emerald find anything yesterday?" Red asked.

"Yes," the woman's eyes seemed to fill with new tears, "but you have to see it for yourself. I get too teared up whenever I think about it. Sorry I'm not of much help."

"It's okay." Yellow reassured her, "At least you've told us where to start." Ruby's mother smiled.

"Sapphire and Emerald, along with what they found yesterday, are over at Birch's lab. Do you know where that is?" The kids nodded, having been there before, "That's good. And hopefully, you can find Ruby. Goodbye!"

"Bye, Mrs. Maple!" Green said, and the door was closed.

"Birch's lab, here we come!" Gold said with a smirk before starting off, where the others followed.

* * *

"Is it done yet?"

"We're close." Magnus scowled.

"Finish it before the Dex Holders leave Hoenn, _or else_." His fearsome glare made the scientist nod quickly before leaving the man to his work. He was greeted at the door to the Science Facility by Arianna when he left.

"Not done yet." he growled to her, where she adopted a similar scowl.

"Oh, I'll get them to stay in Hoenn as long as it takes for those scientists to finish that project." Her face then took on a curious look, "What is the project, anyway?"

"You'll learn at the same time as Frost, and you'll have first crack at it." Gleefully, the girl laughed.

"Can't wait!" she clapped her hands together, "And that gives me the _perfect_ idea of a delay..."

* * *

 _ **Here is the second chapter! Also, something else in here will be different besides the storyline. Can you guess? And R & R, readers!**_


	3. AN

**ATTENTION, REVIEWERS, GUESTS, READERS, FAVORITERS, AND FOLLOWERS! THIS IS AN IMPORTANT ANNOUNCEMENT!**

 **Well, not really, but I needed to get your attention somehow, right? Anyway, I have a challenge for all of you! A while back, I found a picture on DeviantArt by 1sthi1357 made of Dino TK, from my story, _Of Dinos and Digimon_. Last night, when I was looking at it again, it gave me an idea!**

 **I am not a drawing person. I trace, but don't draw. Which is why I want to ask you guys if you could draw for me! Well, not for me, but from my stories.**

 **This is what I mean: you draw things from my stories and post them on DeviantArt, I'll mention them in the story they're from. There is no cost or prize, except maybe a Llama and my eternal happiness!**

 **Here are the rules:**

 **1\. You _MUST_ include my name in the description so I can find it and the name of the story it's from.**

 **2\. It doesn't have to be a good picture, it can be whatever. I want to see what you all can come up with!**

 **3\. You can make multiple works of art, not just one piece.**

 **4\. They can either be character designs, scenes (or comics) from the story, or title pictures.**

 **Now that that's done with, I hope you guys take on the challenge! See you!**


End file.
